[ensembl-dev] VEP and ExAC plugin

Will McLaren wm2 at ebi.ac.uk
Thu Aug 6 10:33:33 BST 2015


Hi Nicolas,

Thanks for the report - some of the headers were getting scrambled
internally.

I've pushed fixes to release/81 of ensembl-tools (the
variant_effect_predictor.pl script) and the ExAC.pm plugin file - please
re-download VEP and re-run the installer.

Regards

Will McLaren
Ensembl Variation

On 5 August 2015 at 17:24, Nicolas Thierry-Mieg <
Nicolas.Thierry-Mieg at imag.fr> wrote:

> Hi all,
>
> I'm experimenting with the ExAC plugin for VEP. I've noticed that I only
> obtain the global ExAC_AF but not the population-specific ExAC_*_AF values
> when using the --vcf option. Withouth this option it works.
> Details follow.
>
>
> For these tests I DL'd the latest VEP v81 available today, used
> INSTALL.pl, installed homo_sapiens_refseq_vep_81_GRCh37.tar.gz as a cache
> as well as the ExAC.pm plugin (both via INSTALL.pl). And I DL'd
> ExAC.r0.3.sites.vep.vcf.gz from the broad ftp.
>
> $ more input.vcf
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
> chr1    26131654        .       G       A       67.09   PASS
>
> $ variant_effect_predictor.pl -i input.vcf -o ttt.vcf --vcf --offline
> --refseq  --plugin
> ExAC,/home/nthierry/Software/ExAC/ExAC.r0.3.sites.vep.vcf.gz  --force
> 2015-08-05 17:34:41 - Read existing cache info
> 2015-08-05 17:34:41 - Loaded plugin: ExAC
> 2015-08-05 17:34:41 - Starting...
> 2015-08-05 17:34:41 - Detected format of input file as vcf
> 2015-08-05 17:34:41 - Read 1 variants into buffer
> 2015-08-05 17:34:41 - Reading transcript data from cache and/or database
> [===============================================]  [ 100% ]
> 2015-08-05 17:34:41 - Retrieved 92 transcripts (0 mem, 236 cached, 0 DB, 0
> duplicates)
> 2015-08-05 17:34:41 - Analyzing chromosome 1
> 2015-08-05 17:34:41 - Analyzing variants
> [===============================================]  [ 100% ]
> 2015-08-05 17:34:41 - Calculating consequences
> 2015-08-05 17:34:41 - Processed 1 total variants (1 vars/sec, 1 vars/sec
> total)
> 2015-08-05 17:34:41 - Wrote stats summary to ttt.vcf_summary.html
> 2015-08-05 17:34:41 - Finished!
>
>
> So, it seems to run OK, but the produced ttt.vcf ends with |||||0.814||| .
> I would expect these (empty) fields to contain values.
>
>
> If I remove --vcf from my command, the output vcf contains
> population-specific allele freqs, as expected, eg:
> ExAC_AF_FIN=0.728;IMPACT=MODERATE;ExAC_AF=0.814;ExAC_AF_OTH=0.816;[...]
>
> As a side note, as you can see without --vcf the fields are called
> ExAC_AF_* , but in the same file they are documented as ExAC_*_AF, eg:
> ## ExAC_EAS_AF  : ExAC East Asian Allele frequency
> This last point is just a minor glitch, but you may want to fix it as well.
>
>
> Regards,
> Nicolas
>
>
> --
> -----------------------------------------------------------
> Nicolas Thierry-Mieg
> Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525
> Pavillon Taillefer, Faculte de Medecine
> 38700 La Tronche, France
> tel: (+33)456.520.067, fax: (+33)456.520.055
> ------------------------------------------------------------
>
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